Public apps 82

pKa model
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Model to predict the pKa of compounds

  • Owner:
    Yojana Gadiya
Running
Dashboard for comparing child-BMI
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Comparing 4 types of the most common reference populations for child sex- and age-adjusted Body Mass Index (BMI)

  • Owner:
    Maja Engsner
Running
DILI Predictor
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DILI Predictor is an open-source app framework built specifically for human drug-induced liver injury (DILI). DILI Predictor employs eleven proxy-DILI labels from in vitro and in vivo datasets along with pharmacokinetic parameters, structural fingerprints and physicochemical parameters as features.

  • Owner:
    Hamza Saeed
Running
starbase
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starbase is a database and toolkit for exploring of large transposable elements in Fungi

  • Owner:
    Adrian Forsythe
Running
Design tool for PbHiT sgRNA vectors
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This site provides a databases of knockout designs targeting the entire Plasmodium berghei protein encoding genome using the PbHiT CRISPR system as described in Jonsdottir et al. DOI: https://doi.org/10.1101/2024.04.20.590404

  • Owner:
    Johan Henriksson
Running
Vector oligo search
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This is a test deployment of the vector oligo search

  • Owner:
    Mattias Nyberg
Running
Dictyostelium discoideum RNA-seq and proteomics developmental time course
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Shiny app for displaying Dictyostelium discoideum RNA-seq and proteomics data, from the publication Edelbroek et al. 2024

  • Owner:
    Jakub Westholm
Running
KG Dashboard
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Dashboard for the R4A Expertise KG

  • Owner:
    Yojana Gadiya
Running
United Kingdom Flower Classification App
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This app allows users to input an image (in jpeg format) of a flower and get a prediction on what type of flower it is from a machine learning model. Top three most likely flower types according to the model’s prediction are shown.

  • Owner:
    Arnold Kochari
Running
BAGS-Shiny
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Biome-specific gene catalogues have been recovered for many environments using shotgun metagenomics, followed by assembly and gene calling on the assembled contigs. We recently proposed a novel mix-assembly strategy, combining individual and co-assembly approaches, and used this approach to assemble an extensive non-redundant gene set from 124 Bal...

  • Owner:
    Luis Fernando Delgado Zambrano
Running
Lee_et_al_2024_supplementary_data
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All the browsable datasets from Lee et al 2024. "Open source, high throughput, targeted in situ transcriptomics"

  • Owner:
    Marco Grillo
Running
ADHD medication among 0-19 year olds in Sweden
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Dashboard plotting the number of people in Sweden aged 0-19 who have have filled a prescription for ADHD medication each year.

  • Owner:
    Arnold Kochari
Running
COVID-19 in Sweden
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This dashboard visualises the spread of COVID-19 in Sweden: confirmed cases, ICU admissions, and deaths between February 2020 and March 2023.

  • Owner:
    Arnold Kochari
Running
cpLogD-v2.0
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Conformal regression model for predicting LogD for drug-like molecules, trained on ChEMBL version 33 with over 2.2M compounds using the CPSign software.

  • Owner:
    Staffan Arvidsson McShane
Running
Ames Mutagenicity Prediction
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Predicts Ames Mutagenicity for a chemical structure using an SVM model with Signatures features via the CPSign modeling tool.

  • Owner:
    Ola Spjuth
Running
RepurposeDrugs
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RepurposeDrugs - an interactive web-based data portal and predictive platform for repurposing mono- and combination therapies.

  • Owner:
    Aleksandr Kushnir
Running
Developmental human heart ISS
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Modelling of cell-type signatures in the developmental human heart

  • Owner:
    Christophe Avenel
Running
Human heart development (ISS)
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Human heart development ISS datasets generated for Lazar et.al 2024.

  • Owner:
    Sergio Marco Salas
Running
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases
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Colorectal cancer usually metastasizes in the liver. Tumor cells can create two types of metastases: desmoplastic (DHGP) or replacement (RHGP). DHGP is characterized by a fibrotic rim that encapsulates the tumor cells and is associated with a better survival. In this project, we found two distinct areas in the rim: an outer area representing a ben...

  • Owner:
    Axel Andersson
Running
ALLIUM
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ALLIUM (ALL subtype Identification Using Machine learning) is a multimodal classifier of molecular subtypes in pediatric acute lymphoblastic leukemia, using DNA methylation (DNAm) and gene expression (GEX) data

  • Owner:
    Mariya Lysenkova Wiklander
SubCellBarcode CoLocal
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Correlation Network

  • Owner:
    Luay Aswad
Running
SubCellBarcode BarCode
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Single Protein Localization

  • Owner:
    Luay Aswad
Running
SubCellBarcode Network
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Network

  • Owner:
    Luay Aswad
Running
SubCellBarcode Download
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Data Download

  • Owner:
    Luay Aswad
Running
SubCellBarcode Heatmap
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Heatmap

  • Owner:
    Luay Aswad
Running
Predgui Multiple Molecules
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Application that allows users to get predictive data about compound (Multiple Molecules)

  • Owner:
    Hamza Saeed
Running
Predgui
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Application that allows users to get predictive data about compound (Single Molecule)

  • Owner:
    Hamza Saeed
Running
Demo of ROC curves PR curves and decision boundaries
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Demo of ROC curves, PR curves, and decision boundaries for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_roc

  • Owner:
    Johan Henriksson
Running
Demo of xgboost and decision trees
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Demo of xgboost and decision trees for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_xgboost

  • Owner:
    Johan Henriksson
Running
DICTrank Predictor
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DICTrank Predictor is an open-source app framework built specifically for human drug-induced cardiotoxicity (DICT).DICTrank Predictor employs physicochemical parameters as feature. For more details look at https://www.biorxiv.org/content/10.1101/2023.10.15.562398v1

  • Owner:
    Hamza Saeed
Running
cpLogD API
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API for model that predicts water–octanol distribution coefficient (logD) for chemical compounds: It is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates

  • Owner:
    Hamza Saeed
Running
PK Predictor
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PK Predictor is an open-source app framework built specifically for predicting human and animal PK parameters

  • Owner:
    Hamza Saeed
Running
SeuratObjectMaker
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A Shiny webapp for creating a Seurat object without programming expertise. Load a count matrix directory, interactively filter on metadata, view results, download Seurat object and results of differential gene expression testing.

  • Owner:
    Rasmus Olofzon
Running
Demo of clustering with Leiden
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Demo of clustering with Leiden for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_clustering

  • Owner:
    Johan Henriksson
Running
Demo of penalized linear models (elastic net)
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Demo of penalized linear models (elastic net) for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_elasticnet

  • Owner:
    Johan Henriksson
Running
Demo of Bayesian linear models
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Demo of Bayesian linear models for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesianlinmod

  • Owner:
    Johan Henriksson
Running
Demo of Bayesian updating
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Demo of Bayesian updating for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesupdate

  • Owner:
    Johan Henriksson
Running
Single Cell Analysis of Inhibitory Efferents of the Lateral Line
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scRNASeq of 55 samples from zebrafish brain. This project aims to characterize expression profile of different cell types.

  • Owner:
    Nima Rafati
Running
Demo of markov chains and HMMs
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Demo of markov chains and HMMs for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_markovchain

  • Owner:
    Johan Henriksson
Running
Demo of the Poisson distribution
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Demo of the Poisson distribution, as relevant for NGS, for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_poisson

  • Owner:
    Johan Henriksson
Running
Demo of statistical distributions
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Demo of statistical distributions for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_statdist

  • Owner:
    Johan Henriksson
Running
Keywords VOS
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Co-occurrence plots created using VOS viewer . There are three plots in total, each based on publications from a different SciLifeLab reporting group (i.e. affiliated researchers, infrastructure units, and SciLifeLab fellows). In each plot, we have considered the KeyWords Plus associated with each paper.

  • Owner:
    Senthilkumar Panneerselvam
Running
TRIDENT
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Predicting chemical ecotoxiticy using AI. DOI: https://doi.org/10.1101/2023.04.17.537138

  • Owner:
    Käll Styrbjörn
Running
Color Balance Checker
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An app to check color balance in indexes for sequencing

  • Owner:
    Alma Hansen
Running
GPGP-Vc
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Shiny app for exploration of the Genome-wide PeptidoGlycan Profiling dataset of Vibrio cholerae mutant library. Access to this app is password protected while it is under peer review.

  • Owner:
    Laura Alvarez
Running
BridgeDb: framework to map identifiers between various biological databases
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The mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. This is a REST service for programmatic access to BridgeDb content, provided with interactive Swagger documentation using OpenAPI. For more info see https://www.bridgedb.org/.

  • Owner:
    Arnold Kochari
Running
Chemid Convert
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Service that provides a REST Api to convert between different chemical notations. More info: https://github.com/DouglasConnect/ChemIdConvert.

  • Owner:
    Hamza Saeed
Running
Adipose Tissue Gene Expression Visualization
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Supplemental interactive visualization of Adipose Tissue Gene expression after exercise. Built using flexdashboard.

  • Owner:
    Leonidas Lundell
Running
PTP: Predictive Target Profile
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API for Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. Refer to https://doi.org/10.3389/fphar.2018.01256 for the paper describing the tool.

  • Owner:
    Hamza Saeed
Running
LymphProg
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A tool to predict the risk of experiencing refractory/relapse disease within two years in DLBCL patients treated with R-CHOP.

  • Owner:
    Hui Wan
Running
RNA-Seq Power
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Power analysis for RNA-Seq experiment. Estimate number of samples required and more.

  • Owner:
    Roy Francis
Running
Imminent myocardial infarction prediction model
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Imminent myocardial infarction prediction model. In patients free from prior cardiovascular disease, we aimed to identify characteristics of an imminent first heart attack and design a prediction model.

  • Owner:
    Stefan Gustafsson
Running
DRE: Cancer Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Geneset Similarity Analysis
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Infection Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Drug Set Enrichment Analysis
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Defect Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Psychiatric Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Other Diseases Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Atrophy Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Syndrome Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Degenerative Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Immune Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Gene Set Enrichment Analysis
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Drug Repurposing Tool
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
DRE: Drug Pathway Database
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This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

  • Owner:
    Lu Pan
Running
MethylR
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A single shiny solution from sequencer data to pathway analysis

  • Owner:
    Jyotirmoy Das
Running
Wellness study CB2030 Systems biology course
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This Shiny app is used the course CB2030 Systems biology at KTH Royal Instute of Technology.

  • Owner:
    Thanadol Sutantiwanichkul
Running
IFNB scRNA-Seq
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IFNB single-cell transcriptomics data

  • Owner:
    Roy Francis
Running
Differential Expression Analysis for Suprcellfatory project
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Trancriptom analysis for Suprcellfactories project

  • Owner:
    Rasool Saghaleyni
Running
Cell Chat
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CellChat's Shiny app which allows interactive exploration of the cell-cell communication that are analyzed by the CellChat R-package

  • Owner:
    Christophe Avenel
Running
CoViMAPP
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CoViMAPP (CoViD-19 Meta-Analysis of Plasma Proteins) is a meta-analysis resource of plasma proteins' alterations in COVID-19.

  • Owner:
    Haris Babacic
Running
OmicLoupe
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OmicLoupe server. See https://quantitativeproteomics.org/omicloupe/ for info about OmicLoupe.

  • Owner:
    Fredrik Levander
Running
igraph_3D
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3D igraph from tsne with variable genes (Data from Tiklova et al. 2016)

  • Owner:
    Nanjiang Shu
Running
Natural Nations
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CitizenScience Project

  • Owner:
    Nanjiang Shu
Running
MetaMEx
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Meta-analysis of skeletal muscle response to exercise and inactivity

  • Owner:
    Nicolas Pillon
Running
NHP Shiny
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Single cell RNA sequencing dataset associated with the manuscript "Amnion signals are essential for mesoderm formation in primates"

  • Owner:
    Nanjiang Shu
Running
LTS project
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scRNA-seq data in: Small molecule screen identifies a salt-inducible kinase inhibitor inducing β-cell proliferation by transiently activating the unfolded protein response

  • Owner:
    Nanjiang Shu
Running
NBIS Support 4884
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Byrnes, Lauren E., et al. Lineage dynamics of murine pancreatic development at single-cell resolution

  • Owner:
    Nanjiang Shu
Running
Gutsy Atlas
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Companion resource to the article, 'An online atlas of human plasma metabolite signatures of gut microbiome composition' by Dekkers et al

  • Owner:
    Koen Dekkers
Running
Boreal Rhizospheric Atlas
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The Boreal Rhizospheric Atlas online tool was created to encourage exploration of a metatranscriptomic dataset of Norway spruce fine roots and their associated fungal communities from nutrient limited and nutrient enriched forest plots of the boreal region of Northern Sweden.

  • Owner:
    Nicolas Delhomme
Running
Mouse metabolite atlas
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The Mouse Organ Metabolite Atlas

  • Owner:
    Tomasz Czuba
Running